Contacts of the helix formed by residues 1359 - 1373 (chain B) in PDB entry 1FP7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1359 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337B LEU* 3.0 38.7 - - - +
1340B HIS* 3.3 21.3 + - - +
1341B GLY* 4.1 0.2 - - - -
1355B ALA 2.7 15.2 + - - -
1358B GLU* 1.3 73.0 - - - +
1360B PHE* 1.3 60.0 + - - +
1362B ASN* 3.3 22.0 - - - +
1504B GLY* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337B LEU* 3.5 19.7 - - + -
1356B LEU 3.2 16.4 + - - +
1357B ARG* 3.0 19.0 + - + +
1358B GLU 2.9 0.4 - - - -
1359B GLY* 1.3 74.3 - - - +
1361B ALA* 1.3 65.2 + - - +
1362B ASN 2.6 8.3 + - - -
1363B LEU* 3.0 26.7 + - + -
1364B GLU* 2.9 67.6 + - + -
1367B ILE* 5.7 1.6 - - + -
1395B LEU* 4.0 9.2 - - + -
1398B LEU* 3.5 57.0 - - + -
1399B CYS* 3.9 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357B ARG 3.6 3.2 + - - +
1358B GLU* 2.9 16.8 + - - +
1360B PHE* 1.3 77.3 - - - +
1362B ASN* 1.3 65.2 + - - +
1364B GLU* 3.4 14.2 - - - +
1365B LYS* 2.9 22.2 + - - +
1505B ARG* 3.8 30.8 - - + +
1507B ARG* 5.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B ILE* 3.5 14.6 - - - +
1066B THR* 3.0 48.0 + - - +
1337B LEU* 5.0 1.0 - - + +
1340B HIS* 3.7 28.6 + - + +
1359B GLY 3.3 16.8 + - - +
1360B PHE 2.6 3.8 + - - -
1361B ALA* 1.3 71.4 - - - +
1363B LEU* 1.3 76.5 + - - +
1365B LYS* 2.8 20.8 + - - +
1366B HIS* 3.5 5.0 + - - -
1496B PHE* 3.5 14.8 - - - -
1504B GLY* 3.4 19.1 - - - +
1505B ARG* 4.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B ILE* 3.9 22.0 - - + -
1330B ILE* 3.5 26.2 - - + +
1331B VAL 4.1 0.7 - - - +
1332B ALA* 4.1 16.4 - - + -
1337B LEU* 4.0 9.6 - - + +
1359B GLY 4.4 0.2 + - - -
1360B PHE* 3.0 31.5 + - + +
1362B ASN* 1.3 80.1 - - - +
1364B GLU* 1.3 54.7 + - - +
1365B LYS 3.3 0.3 + - - -
1366B HIS* 3.4 6.2 + - - +
1367B ILE* 2.7 58.5 + - + +
1379B VAL* 4.2 21.3 - - + -
1381B ILE* 5.2 0.2 - - + -
1395B LEU* 4.4 12.3 - - + -
1399B CYS* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360B PHE* 2.9 50.6 + - + +
1361B ALA* 3.4 10.8 - - - +
1362B ASN 2.9 0.8 + - - -
1363B LEU* 1.3 78.0 - - - +
1365B LYS* 1.3 60.6 + - - +
1367B ILE* 3.1 18.9 - - + +
1368B GLU* 3.1 33.1 - - + +
1398B LEU* 5.0 3.5 - - - +
1401B LYS* 5.4 9.0 - - + +
1505B ARG* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361B ALA 2.9 11.0 + - - +
1362B ASN 2.8 9.4 + - - +
1364B GLU* 1.3 68.1 - - - +
1366B HIS* 1.3 68.6 + - - +
1368B GLU* 2.8 35.0 + - - +
1369B ASN* 3.2 14.9 + - - +
1372B LYS* 4.6 6.5 - - - +
1456B THR 4.9 1.0 + - - -
1457B GLU* 2.6 30.7 + - - +
1458B ILE 3.3 13.2 - - - -
1459B TYR 4.2 8.3 - - - +
1460B GLY* 4.8 3.4 - - - -
1496B PHE* 3.5 37.2 - - + -
1505B ARG* 3.6 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B ILE* 3.3 29.1 + - - -
1066B THR* 2.3 31.1 + - - -
1306B ALA* 3.8 20.3 - - + +
1307B ASP* 3.4 29.8 + - + +
1330B ILE* 3.5 19.3 - - + -
1362B ASN* 3.5 16.4 + - - -
1363B LEU* 3.4 2.1 + - - +
1365B LYS* 1.3 75.2 - - - +
1367B ILE* 1.3 65.5 + - - +
1369B ASN* 2.8 12.8 + - - +
1370B ILE* 2.7 28.6 + - + +
1496B PHE* 3.1 21.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330B ILE* 3.9 14.6 - - + -
1360B PHE* 5.7 2.0 - - + -
1363B LEU* 2.7 51.8 - - + +
1364B GLU* 3.1 19.7 - - + +
1366B HIS* 1.3 73.8 - - - +
1368B GLU* 1.3 63.6 + - + +
1370B ILE* 3.3 10.4 - - - +
1371B GLY* 3.2 17.0 + - - -
1377B ALA* 5.3 12.0 - - + +
1379B VAL* 4.9 12.3 - - + -
1401B LYS* 4.3 26.9 - - + -
1402B ALA* 5.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1364B GLU* 3.1 30.3 - - - +
1365B LYS* 2.8 20.5 + - + +
1367B ILE* 1.3 73.3 - - - +
1369B ASN* 1.3 63.9 + - - +
1371B GLY* 3.3 4.3 + - - -
1372B LYS* 3.2 31.2 + - - +
1401B LYS* 4.1 26.8 + - + +
1505B ARG* 3.7 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306B ALA 5.9 2.9 - - - +
1365B LYS* 3.3 28.9 + - - +
1366B HIS* 2.8 18.5 + - - +
1368B GLU* 1.3 69.5 - - - +
1370B ILE* 1.3 72.2 + - - +
1372B LYS* 2.8 27.8 + - - +
1373B PHE* 3.4 10.7 - - + -
1457B GLU 2.5 26.5 - - - +
1458B ILE* 2.8 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063B THR* 4.7 2.5 - - + -
1306B ALA* 5.1 7.0 - - + -
1310B ALA* 6.1 1.8 - - + -
1314B TYR* 4.6 6.5 - - + +
1328B THR* 4.4 13.7 - - + -
1329B VAL 4.2 5.8 - - - +
1330B ILE* 3.3 42.2 - - + -
1366B HIS* 2.7 24.7 + - + +
1367B ILE* 3.3 16.8 - - + +
1369B ASN* 1.3 74.6 - - - +
1371B GLY* 1.3 66.3 + - - +
1373B PHE* 3.0 21.6 + - - +
1375B VAL* 3.9 13.6 - - + +
1376B PRO 3.4 24.7 - - - +
1377B ALA* 3.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367B ILE 3.2 8.9 + - - -
1368B GLU 3.7 4.0 - - - -
1369B ASN 3.2 0.8 - - - -
1370B ILE* 1.3 80.8 - - - +
1372B LYS* 1.3 50.1 + - - +
1373B PHE 2.7 0.3 + - - -
1374B GLY* 2.6 33.4 + - - -
1375B VAL 3.7 13.0 + - - -
1377B ALA* 5.5 0.9 - - - +
1433B ARG* 5.8 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365B LYS* 4.6 5.4 - - - +
1368B GLU* 3.2 22.0 + - - +
1369B ASN* 2.8 29.4 + - + +
1371B GLY* 1.3 68.7 - - - +
1373B PHE* 1.3 56.2 + - + -
1374B GLY 3.2 1.3 - - - -
1438B HIS* 3.3 16.8 + - - -
1440B LEU* 4.1 22.1 - - + +
1457B GLU* 2.9 60.6 + - + +
1458B ILE* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310B ALA* 6.1 0.2 - - + -
1311B GLU* 3.7 26.7 - - + -
1314B TYR* 3.7 53.6 - + + -
1315B ASP* 3.7 15.3 - - - -
1369B ASN* 3.4 15.9 - - + -
1370B ILE* 3.0 9.2 + - - +
1371B GLY 2.7 4.2 + - - -
1372B LYS* 1.3 73.3 - - - +
1374B GLY* 1.3 60.5 + - - +
1375B VAL* 4.1 6.8 - - + +
1437B PHE* 4.2 2.5 - + + -
1438B HIS* 3.0 38.7 + - - +
1439B VAL 4.7 0.2 - - - -
1440B LEU* 3.3 46.4 - - + +
1458B ILE* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il